So, this might just be impossible in the engine, or a bad idea, or both, but here's somthing that I'd really love to see.

When playing against an AI, fleets take pretty even damage, which is nice for the feel of the game, but it feels wrong because tactically they should go for those special ability using caps ASAP, especially ones with super nifty abilities like the Marza or the Vasari Carrier healing everyone in sight.  When playing against players, the opposite is true; it's almost not worth it to have any caps because they'll get headshotted in seconds.  The role of caps basically becomes "a cheap way to get your first couple colonies set up."

To make the experience more even and a little deeper as well, what about having capital ships be allowed escorts?  The basic idea would be that the cloud of escorts would provide some damage mitigation on the cap, and have their damage nerfed as compensation.  I'd leave the details up to the people who have to code it, but here's an example of how it might work:

Someone decides by fiat on a number that represents full coverage, like maybe 100 points worth of ships.  Ships assigned to a fleet with a cap ship auto-target the cap's assailants and take something like a 50% damage nerf and an abilities disabled nerf (to avoid the abuse of putting non-damage dealing ships in the escort).  Damage directed at the cap is instead directed against the escorts, one by one, with (100-<fleet points currently in the escort>)% slopping over to the cap.  Obviously the cap fleets are now tight cohesion and jump together by default.

This means that you're now going to be manipulating multiple fleets a lot, but that's okay; it's not that hard to set more than one fleet to a group, or maybe there's some kind of toggle in the tactics page.  Maybe some kinds of ships take a lower damage nerf due to being inherently escort-ey (like Guardians or flaks).  But the basic idea is that there's some kind of way to get your high level caps into battle against a human opponent.  Maybe it's painful, maybe it's not worth it in every situation, but it'd be nice to have the option.